Merge local changes: add web interface and algorithm updates

Author: dsmutin

.gitignore

@@ -74,3 +74,4 @@ PROBEst.Rproj
 .Rproj.user
 .Rhistory
 articles.tar.bz2
+data/databases/articles/artificial_database_structure

app/.gitignore

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+# PROBESt Web Application
+
+A web-based interface for the PROBESt probe generation and optimization tool.
+
+## Features
+
+- **User-friendly web interface** for all PROBESt parameters
+- **File upload** for input FASTA, BLAST databases, and contig tables
+- **Real-time processing** with progress indicators
+- **Results visualization** showing top 5 best probes
+- **Download results** as a ZIP file containing all output files
+
+## Installation
+
+1. Install Flask and required dependencies:
+```bash
+pip install flask werkzeug
+```
+
+2. Ensure all PROBESt dependencies are installed (see main README.md)
+
+3. Make sure `primer3_core` and `blastn` are available in your PATH
+
+## Running the Application
+
+From the project root directory:
+
+```bash
+cd app
+python app.py
+```
+
+The application will be available at `http://localhost:5000`
+
+## Usage
+
+### Required Inputs
+
+1. **Input FASTA File**: Input FASTA file for probe generation (.fna recommended)
+   - Can be a single FASTA file (.fa, .fasta, .fna) or an archive (.zip, .tar.gz) containing FASTA files
+   
+2. **True Base Archive**: Archive containing FASTA files for primer adjustment
+   - Must be a .zip or .tar.gz archive
+   - Archive should contain one or more FASTA files (.fa, .fasta, .fna, optionally gzipped)
+   - The archive will be automatically preprocessed using `prep_db.sh` to create a BLAST database
+   
+3. **False Base Archive(s)**: Archive(s) containing FASTA files for non-specific testing
+   - Must be .zip or .tar.gz archives
+   - Can upload multiple archives
+   - Each archive will be automatically preprocessed using `prep_db.sh` to create BLAST databases
+   
+**Note**: The contig table is automatically generated from the true base archive during preprocessing.
+
+### Optional Parameters
+
+The web interface provides access to all optional parameters:
+
+- **Basic Parameters**: Threads, Algorithm type
+- **Evolutionary Algorithm**: Iterations, mutation rates, set sizes
+- **Primer3 Parameters**: Primer size ranges, product size
+- **BLAST Parameters**: Word size, scoring parameters
+- **Probe Check Parameters**: Mismatch thresholds, identity requirements
+
+### Results
+
+After processing:
+
+1. **Top 5 Probes** are displayed on screen with:
+   - Probe name
+   - Hit count (number of matches)
+   - Sequence length
+   - Full sequence
+
+2. **Download Results** button provides a ZIP file containing:
+   - `output.fa`: Final probe sequences
+   - `stats.csv`: Iteration statistics
+   - All intermediate files from the pipeline
+
+## File Structure
+
+```
+app/
+├── app.py              # Flask application
+├── templates/
+│   └── index.html     # Main web interface
+├── static/
+│   ├── style.css      # Styling
+│   └── script.js      # Client-side JavaScript
+├── uploads/           # Temporary file uploads (created automatically)
+└── results/            # Processing results (created automatically)
+```
+
+## Notes
+
+- Uploaded files are stored temporarily and cleaned up after processing
+- Processing may take several minutes depending on input size and parameters
+- The application uses session-based file management for security
+
+